Molecule file manipulation and conversion program

for the Windows platform

version 5.6.3

What is Mol2Mol?

About two decades ago, at the end of the 80's, the different molecular modelling programs have started widely to spread. These programs use different file formats to hold the coordinate and atomic data, and each format follows unique syntax rules, which prevents the direct transfer of the molecules between the different applications. It was a serious drawback of the early programs, but even today there is a need for the transformation of molecule files. This led to the development of the original Mol2Mol several years ago.

The current version of Mol2Mol™ recognizes, reads and writes about 50 different file formats and subformats. It contains a simple graphic display module to inspect the currently loaded molecule. It possesses some chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added to the heavy atoms. Problematic files can be corrected within Mol2mol or as ASCII files by calling directly your favourite text editor.

Mol2Mol is more than just a simple conversion system

• Calculation of basic geometrical data: distances, angles, dihedral angles;
• Calculation of atom pyramidalities, angle of rings, distances from least square planes, ring puckerings;
• Changing of bond types, atom types;
• Add or delete hydrogens, structural waters;
• Add hydrogens in pH dependent mode;
• Slicing of biopolymers or multiple files to individual molecules;
• Batch or many-to-many conversion;
• Merging of individual simple files to multiple ones;
• Browsing multiple files;
• Conversion of multiple structural files;
• Conversion of proteins to "backbone molecules", Ramachandran plot;
• Checking of peptide backbone geometry, adding CH₃, CH₂ centroid pseudo atoms;
• Manual editing of problematic files... and many others.

Main window:

Graphics window: